def viewSingleRecord(cls, record, research_mode):
view_aspects = defineViewSchema()
view_checker = ViewDataChecker(view_aspects)
view_checker.regValue(0, record)
rep_out = StringIO()
is_ok = view_checker.finishUp(rep_out)
if not is_ok:
logging.error("Single record annotation failed:\n" +
rep_out.getvalue())
assert is_ok
aspects = AspectSetH.load(view_aspects.dump())
return aspects.getViewRepr(record, research_mode)
def __init__(self, data_vault, dataset_info, dataset_path):
self.mDataVault = data_vault
self.mDataInfo = dataset_info
self.mLock = Lock()
self.mName = dataset_info["name"]
self.mDSKind = dataset_info["kind"]
self.mTotal = dataset_info["total"]
self.mMongoName = dataset_info["mongo"]
self.mAspects = AspectSetH.load(dataset_info["view_schema"])
self.mFltSchema = dataset_info["flt_schema"]
self.mPath = dataset_path
self.mVData = IndexBZ2(self.mPath + "/vdata.ixbz2")
self.mFamilyInfo = FamilyInfo.load(dataset_info.get("family"))
def __init__(self, data_vault, dataset_info, dataset_path):
self.mDataVault = data_vault
self.mDataInfo = dataset_info
self.mLock = Lock()
self.mName = dataset_info["name"]
self.mDSKind = dataset_info["kind"]
self.mTotal = dataset_info["total"]
self.mMongoAgent = (data_vault.getApp().getMongoConnector().getDSAgent(
dataset_info["mongo"], dataset_info["kind"]))
self.mAspects = AspectSetH.load(dataset_info["view_schema"])
self.mFltSchema = dataset_info["flt_schema"]
self.mPath = dataset_path
self.mVData = IndexBZ2(self.mPath + "/vdata.ixbz2")
self.mFamilyInfo = FamilyInfo(dataset_info["meta"]["samples"],
dataset_info["meta"].get("proband"))
tuneAspects(self, self.mAspects)
def __init__(self,
data_vault,
dataset_info,
dataset_path,
sol_pack_name=None):
SolutionBroker.__init__(
self, dataset_info["meta"].get("data_schema", "CASE"),
dataset_info.get("modes"))
self.addModes(data_vault.getApp().getRunModes())
self.mDataVault = data_vault
self.mDataInfo = dataset_info
self.mName = dataset_info["name"]
self.mDSKind = dataset_info["kind"]
self.mTotal = dataset_info["total"]
self.mMongoAgent = (data_vault.getApp().getMongoConnector().getDSAgent(
dataset_info["mongo"], dataset_info["kind"]))
self.mAspects = AspectSetH.load(dataset_info["view_schema"])
self.mFltSchema = dataset_info["flt_schema"]
self.mPath = dataset_path
self.mFInfo = self.mDataVault.checkFileStat(self.mPath +
"/dsinfo.json")
if self.getDataSchema() == "FAVOR" and self.mDSKind == "xl":
self.mRecStorage = FavorStorage(
self.getApp().getOption("favor-url"))
else:
self.mRecStorage = DataDiskStorage(self, self.mPath)
self.mFamilyInfo = FamilyInfo(dataset_info["meta"])
if (self.mDataInfo.get("zygosity_var")
and 1 < len(self.mFamilyInfo) <= 10):
self.addModes({"ZYG"})
self.mZygSupport = None
self.mViewContext = dict()
if self.mFamilyInfo.getCohortList():
self.mViewContext["cohorts"] = self.mFamilyInfo.getCohortMap()
view_aspect = AnfisaConfig.configOption("view.cohorts.aspect")
self.mAspects[view_aspect]._setViewColMode("cohorts")
completeDsModes(self)
tuneAspects(self, self.mAspects)